load.bayou: Loads a bayou object

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Loads a bayou object

Description

load.bayou loads a bayouFit object that was created using bayou.mcmc()

Usage

load.bayou(
  bayouFit,
  saveRDS = TRUE,
  file = NULL,
  cleanup = FALSE,
  ref = FALSE,
  verbose = TRUE
)

Arguments

bayouFit	An object of class bayouFit produced by the function bayou.mcmc()
saveRDS	A logical indicating whether the resulting chains should be saved as an *.rds file
file	An optional filename (possibly including path) for the saved *.rds file
cleanup	A logical indicating whether the files produced by bayou.mcmc() should be removed.
ref	A logical indicating whether a reference function is also in the output
verbose	Determines whether information is outputted to the console for the user to view

Details

If both save.Rdata is FALSE and cleanup is TRUE, then load.bayou will trigger a warning and ask for confirmation. In this case, if the results of load.bayou() are not stored in an object, the results of the MCMC run will be permanently deleted.

Value

A list of class '"bayouMCMC"' containing:

gen

A numeric vector of sampled MCMC generations.

lnL

A numeric vector of log-likelihood values.

prior

A numeric vector of prior probabilities.

sb

A list of shift locations sampled across the MCMC chain.

loc

A list of relative shift locations on branches.

t2

A list of new optima values after shifts.

rjpars

A list of reversible-jump parameters sampled at each step.

(Other parameters)

Additional parameters specific to the model used in 'bayou.mcmc()'.

bayou documentation built on June 10, 2025, 5:13 p.m.